1
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Pan X, Wang J, Zhang K, Sun P, Shi J, Zhi J, Cai Z, Li Z, Wang D, Tong B, Dong Y. Differential detection of H1N1 virus spiker proteins by two hexaphenylbutadiene isomers based on size-matching principle. Anal Chim Acta 2024; 1299:342452. [PMID: 38499411 DOI: 10.1016/j.aca.2024.342452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/05/2024] [Accepted: 03/05/2024] [Indexed: 03/20/2024]
Abstract
As one of the high pathogenic influenza viruses, H1N1 virus easily induces to serious diseases, even leading to death. To date, all detection methods for H1N1 virus had shortcomings, including high equipment cost, time consumption, and etc. Therefore, a novel detection method should be established to achieve more convenient, rapid, and low-cost detection. In this work, an isomer of HPBmN-I with aggregation-induced emission characteristic was firstly synthesized on the basis of our previous reported HPBpN-I. The results showed that HPBmN-I only selectively binds to N1 in the presence of H1, while HPBpN-I can exhibit total fluorescence response to H1 and N1 in H1/N1 mixture. The limited of detection (LOD) of HPBmN-I to N1 was estimated to be 20.82 ng/mL in normal saline (NS) according to the IUPAC-based approach. The simulation calculations based on molecular docking revealed that four HPBmN-I molecules combine well with the hydrophobic cavity of N1 and achieve the fluorescence enhancement due to size matching with each other. The combination of HPBpN-I and HPBmN-I as probes was successfully used to quantitatively detect H1 and N1 in real H1N1 virus. Compared to enzyme-linked immunosorbent assay (ELISA) method, the established method not only showed the same detection accuracy but also had the advantages of real-time, ease of preparation, and low-cost, demonstrating potential market prospects.
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Affiliation(s)
- Xiaoling Pan
- Beijing Key Laboratory of Construction Tailorable Advanced Functional Materials and Green Applications, School of Material Science & Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China; Department of Nanomedicine & Shanghai Key Lab of Cell Engineering, Naval Medical University, Shanghai, 200433, China
| | - Jian Wang
- Beijing Key Laboratory of Construction Tailorable Advanced Functional Materials and Green Applications, School of Material Science & Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Kai Zhang
- Beijing Key Laboratory of Construction Tailorable Advanced Functional Materials and Green Applications, School of Material Science & Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Peng Sun
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Jianbing Shi
- Beijing Key Laboratory of Construction Tailorable Advanced Functional Materials and Green Applications, School of Material Science & Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Junge Zhi
- School of Chemistry, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Zhengxu Cai
- Beijing Key Laboratory of Construction Tailorable Advanced Functional Materials and Green Applications, School of Material Science & Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Zi Li
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China
| | - Bin Tong
- Beijing Key Laboratory of Construction Tailorable Advanced Functional Materials and Green Applications, School of Material Science & Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China.
| | - Yuping Dong
- Beijing Key Laboratory of Construction Tailorable Advanced Functional Materials and Green Applications, School of Material Science & Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China.
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2
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Schneider HJ. Distinction and Quantification of Noncovalent Dispersive and Hydrophobic Effects. Molecules 2024; 29:1591. [PMID: 38611870 PMCID: PMC11013637 DOI: 10.3390/molecules29071591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
The possibilities of comparing computational results of noncovalent interactions with experimental data are discussed, first with respect to intramolecular interactions. For these a variety of experimental data such as heats of formation, crystal sublimation heats, comparison with energy minimized structures, and spectroscopic data are available, but until now largely have not found widespread application. Early force field and QM/MP2 calculations have already shown that the sublimation heats of hydrocarbons can be predicted with an accuracy of ±1%. Intermolecular interactions in solution or the gas phase are always accompanied by difficult to compute entropic contributions, like all associations between molecules. Experimentally observed T∆S values contribute 10% to 80% of the total ∆G, depending on interaction mechanisms within the complexes, such as, e.g., hydrogen bonding and ion pairing. Free energies ∆G derived from equilibrium measurements in solution allow us to define binding increments ∆∆G, which are additive and transferable to a variety of supramolecular complexes. Data from more than 90 equilibrium measurements of porphyrin receptors in water indicate that small alkanes do not bind to the hydrophobic flat surfaces within a measuring limit of ∆G = ±0.5 kJ/mol, and that 20 functions bearing heteroatoms show associations by dispersive interactions with up to ∆G = 8 kJ/mol, roughly as a function of their polarizability. Aromatic systems display size-dependent affinities ∆G as a linear function of the number of π-electrons.
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Affiliation(s)
- Hans-Jörg Schneider
- FR Organische Chemie, Universität des Saarlandes, D 66123 Saarbrücken, Germany
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3
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Costa-Tuna A, Chaves OA, Almeida ZL, Cunha RS, Pina J, Serpa C. Profiling the Interaction between Human Serum Albumin and Clinically Relevant HIV Reverse Transcriptase Inhibitors. Viruses 2024; 16:491. [PMID: 38675834 PMCID: PMC11054712 DOI: 10.3390/v16040491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/06/2024] [Accepted: 03/13/2024] [Indexed: 04/28/2024] Open
Abstract
Tenofovir (TFV) is the active form of the prodrugs tenofovir disoproxil fumarate (TDF) and tenofovir alafenamide (TAF), both clinically prescribed as HIV reverse transcriptase inhibitors. The biophysical interactions between these compounds and human serum albumin (HSA), the primary carrier of exogenous compounds in the human bloodstream, have not yet been thoroughly characterized. Thus, the present study reports the interaction profile between HSA and TFV, TDF, and TAF via UV-Vis, steady-state, and time-resolved fluorescence techniques combined with isothermal titration calorimetry (ITC) and in silico calculations. A spontaneous interaction in the ground state, which does not perturb the microenvironment close to the Trp-214 residue, is classified as weak. In the case of HSA/TFV and HSA/TDF, the binding is both enthalpically and entropically driven, while for HSA/TAF, the binding is only entropically dominated. The binding constant (Ka) and thermodynamic parameters obtained via ITC assays agree with those obtained using steady-state fluorescence quenching measurements, reinforcing the reliability of the data. The small internal cavity known as site I is probably the main binding pocket for TFV due to the low steric volume of the drug. In contrast, most external sites (II and III) can better accommodate TAF due to the high steric volume of this prodrug. The cross-docking approach corroborated experimental drug-displacement assays, indicating that the binding affinity of TFV and TAF might be impacted by the presence of different compounds bound to albumin. Overall, the weak binding capacity of albumin to TFV, TDF, and TAF is one of the main factors for the low residence time of these antiretrovirals in the human bloodstream; however, positive cooperativity for TAF and TDF was detected in the presence of some drugs, which might improve their residence time (pharmacokinetic profile).
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Affiliation(s)
- Andreia Costa-Tuna
- CQC-IMS, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal; (A.C.-T.); (Z.L.A.); (R.S.C.); (J.P.)
| | - Otávio A. Chaves
- CQC-IMS, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal; (A.C.-T.); (Z.L.A.); (R.S.C.); (J.P.)
- Laboratory of Immunopharmacology, Centro de Pesquisa, Inovação e Vigilância em COVID-19 e Emergências Sanitárias (CPIV), Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro 21040-361, RJ, Brazil
| | - Zaida L. Almeida
- CQC-IMS, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal; (A.C.-T.); (Z.L.A.); (R.S.C.); (J.P.)
| | - Rita S. Cunha
- CQC-IMS, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal; (A.C.-T.); (Z.L.A.); (R.S.C.); (J.P.)
| | - João Pina
- CQC-IMS, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal; (A.C.-T.); (Z.L.A.); (R.S.C.); (J.P.)
| | - Carlos Serpa
- CQC-IMS, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal; (A.C.-T.); (Z.L.A.); (R.S.C.); (J.P.)
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4
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Pan F, Li X, Tuersuntuoheti T, Zhao L, Liu M, Fang X, Peng W, Tian W. Self-assembled condensed tannins supramolecular system can adsorb cholesterol micelles to promote cholesterol excretion. Int J Biol Macromol 2023; 253:126549. [PMID: 37659485 DOI: 10.1016/j.ijbiomac.2023.126549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/14/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023]
Abstract
In this study, the cholesterol (CH)-lowering behavioral mechanisms and drivers of condensed tannins (CTs) were revealed using a molecular aggregation theoretical model combined with in vitro experiments, as well as the CH-lowering effects of CTs validated based on animal experiments. Theoretical model results indicated that CTs can spontaneously aggregate to form supramolecular systems, can break CH micelles and form larger aggregates, a behavior driven by van der Waals forces and hydrogen bonds; DLS and TEM results confirmed that the presence of CH leads to a larger particle size of CTs and the formation of large aggregates; thermodynamic analysis and ITC revealed that the adsorption of CH by CTs is a spontaneous reaction driven by hydrogen bonds and hydrophobic forces; Animal experiments and fecal biochemical parameters further confirmed that the intake of CTs can reduce CH absorption and promotes CH excretion. Overall, this study reveals the CH-lowering behavioral mechanism of CTs from the perspective of molecular aggregation behavior.
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Affiliation(s)
- Fei Pan
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China
| | - Xiangxin Li
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China.
| | - Tuohetisayipu Tuersuntuoheti
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, 100048, People's Republic of China
| | - Lei Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, 100048, People's Republic of China
| | - Mengyao Liu
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China
| | - Xiaoming Fang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China
| | - Wenjun Peng
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China.
| | - Wenli Tian
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China.
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5
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Knight AL, Widjaja V, Lisi GP. Temperature as a modulator of allosteric motions and crosstalk in mesophilic and thermophilic enzymes. Front Mol Biosci 2023; 10:1281062. [PMID: 37877120 PMCID: PMC10591084 DOI: 10.3389/fmolb.2023.1281062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 09/27/2023] [Indexed: 10/26/2023] Open
Abstract
Mesophilic and thermophilic enzyme counterparts are often studied to understand how proteins function under harsh conditions. To function well outside of standard temperature ranges, thermophiles often tightly regulate their structural ensemble through intra-protein communication (via allostery) and altered interactions with ligands. It has also become apparent in recent years that the enhancement or diminution of allosteric crosstalk can be temperature-dependent and distinguish thermophilic enzymes from their mesophilic paralogs. Since most studies of allostery utilize chemical modifications from pH, mutations, or ligands, the impact of temperature on allosteric function is comparatively understudied. Here, we discuss the biophysical methods, as well as critical case studies, that dissect temperature-dependent function of mesophilic-thermophilic enzyme pairs and their allosteric regulation across a range of temperatures.
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Affiliation(s)
| | | | - George P. Lisi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States
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6
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Plikusiene I, Maciulis V, Vertelis V, Juciute S, Balevicius S, Ramanavicius A, Talbot J, Ramanaviciene A. Revealing the SARS-CoV-2 Spike Protein and Specific Antibody Immune Complex Formation Mechanism for Precise Evaluation of Antibody Affinity. Int J Mol Sci 2023; 24:13220. [PMID: 37686023 PMCID: PMC10487573 DOI: 10.3390/ijms241713220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/04/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023] Open
Abstract
The profound understanding and detailed evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (SCoV2-S) protein and specific antibody interaction mechanism is of high importance in the development of immunosensors for COVID-19. In the present work, we studied a model system of immobilized SCoV2-S protein and specific monoclonal antibodies by molecular dynamics of immune complex formation in real time. We simultaneously applied spectroscopic ellipsometry and quartz crystal microbalance with dissipation to reveal the features and steps of the immune complex formation. We showed direct experimental evidence based on acoustic and optical measurements that the immune complex between covalently immobilized SCoV2-S and specific monoclonal antibodies is formed in two stages. Based on these findings it was demonstrated that applying a two-step binding mathematical model for kinetics analysis leads to a more precise determination of interaction rate constants than that determined by the 1:1 Langmuir binding model. Our investigation showed that the equilibrium dissociation constants (KD) determined by a two-step binding model and the 1:1 Langmuir model could differ significantly. The reported findings can facilitate a deeper understanding of antigen-antibody immune complex formation steps and can open a new way for the evaluation of antibody affinity towards corresponding antigens.
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Affiliation(s)
- Ieva Plikusiene
- NanoTechnas-Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania (S.J.)
- State Research Institute Center for Physical Sciences and Technology, Saulėtekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Vincentas Maciulis
- NanoTechnas-Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania (S.J.)
- State Research Institute Center for Physical Sciences and Technology, Saulėtekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Vilius Vertelis
- State Research Institute Center for Physical Sciences and Technology, Saulėtekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Silvija Juciute
- NanoTechnas-Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania (S.J.)
| | - Saulius Balevicius
- State Research Institute Center for Physical Sciences and Technology, Saulėtekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Arunas Ramanavicius
- NanoTechnas-Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania (S.J.)
- State Research Institute Center for Physical Sciences and Technology, Saulėtekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Julian Talbot
- Laboratoire de Physique Théorique de la Matière Condensée, Sorbonne Université, UMR 7600, 4 Place Jussieu, CEDEX 05, 75252 Paris, France
| | - Almira Ramanaviciene
- NanoTechnas-Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko Str. 24, LT-03225 Vilnius, Lithuania (S.J.)
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7
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Plikusiene I, Maciulis V, Juciute S, Ramanavicius A, Ramanaviciene A. Study of SARS-CoV-2 Spike Protein Wild-Type and the Variants of Concern Real-Time Interactions with Monoclonal Antibodies and Convalescent Human Serum. BIOSENSORS 2023; 13:784. [PMID: 37622870 PMCID: PMC10452135 DOI: 10.3390/bios13080784] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023]
Abstract
The spike (S) protein and its receptor-binding domain (RBD) of the coronavirus SARS-CoV-2 have been continually evolving, yielding the majority of significant missense mutations and new variants of concern. In this study, we examined how monoclonal antibodies against RBD (mAbs-SCoV2-RBD) and polyclonal antibodies present in convalescent human serum specifically interact with the S protein of wild-type and SARS-CoV-2 variants of concern (VOCs) in real time and how this can be reflected through surface mass density. Moreover, we combined two distinct, label-free measurement techniques: one based on changes in surface electromagnetic waves after reflection from the surface, and the other on changes in acoustic waves. The results demonstrated that dry surface mass density (ΓSE) of mAbs-SCoV2-RBD attached to the RBD of the S protein decreases three-fold, from 148 ng/cm2 to 46 ng/cm2, due to the B.1.351 or so-called beta mutation of coronavirus and its S protein (SCoV2-β). Consequently, the obtained wet mass ΓQCM-D resulted in values two times lower, from 319 ng/cm2 to 158 ng/cm2, and the hydration of mAbs-SCoV2-RBD/SCoV2-β immune complex was 70.88%. Conversely, when polyclonal antibodies present in convalescent human serum form immune complexes with the S protein of SARS-CoV-2 variants of concern, the ΓSE decreased from 279 ng/cm2 to 249 ng/cm2, and ΓQCM-D from 1545 ng/cm2 to 1366 ng/cm2. These results can give insights into the differences between the interaction of monoclonal and polyclonal antibodies with SARS-CoV-2 VOCs.
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Affiliation(s)
- Ieva Plikusiene
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, LT-03225 Vilnius, Lithuania
- State Research Institute Center for Physical and Technological Sciences, Sauletekio ave. 3, LT-10257 Vilnius, Lithuania
| | - Vincentas Maciulis
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, LT-03225 Vilnius, Lithuania
- State Research Institute Center for Physical and Technological Sciences, Sauletekio ave. 3, LT-10257 Vilnius, Lithuania
| | - Silvija Juciute
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, LT-03225 Vilnius, Lithuania
| | - Arunas Ramanavicius
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, LT-03225 Vilnius, Lithuania
| | - Almira Ramanaviciene
- NanoTechnas—Center of Nanotechnology and Materials Science, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, LT-03225 Vilnius, Lithuania
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8
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Nydegger DT, Pujol-Giménez J, Kandasamy P, Vogt B, Hediger MA. Applications of the Microscale Thermophoresis Binding Assay in COVID-19 Research. Viruses 2023; 15:1432. [PMID: 37515120 PMCID: PMC10386446 DOI: 10.3390/v15071432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
As the COVID-19 pandemic progresses, new variants of SARS-CoV-2 continue to emerge. This underscores the need to develop optimized tools to study such variants, along with new coronaviruses that may arise in the future. Such tools will also be instrumental in the development of new antiviral drugs. Here, we introduce microscale thermophoresis (MST) as a reliable and versatile tool for coronavirus research, which we demonstrate through three different applications described in this report: (1) binding of the SARS-CoV-2 spike receptor binding domain (RBD) to peptides as a strategy to prevent virus entry, (2) binding of the RBD to the viral receptor ACE2, and (3) binding of the RBD to ACE2 in complex with the amino acid transporter SLC6A20/SIT1 or its allelic variant rs61731475 (p.Ile529Val). Our results demonstrate that MST is a highly precise approach to studying protein-protein and/or protein-ligand interactions in coronavirus research, making it an ideal tool for studying viral variants and developing antiviral agents. Moreover, as shown in our results, a unique advantage of the MST assay over other available binding assays is the ability to measure interactions with membrane proteins in their near-native plasma membrane environment.
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Affiliation(s)
- Damian T Nydegger
- Department of Nephrology and Hypertension, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland
- Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland
| | - Jonai Pujol-Giménez
- Department of Nephrology and Hypertension, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland
- Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland
| | - Palanivel Kandasamy
- Department of Nephrology and Hypertension, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland
- Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland
| | - Bruno Vogt
- Department of Nephrology and Hypertension, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland
- Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland
| | - Matthias A Hediger
- Department of Nephrology and Hypertension, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland
- Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland
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9
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Characterization of the Binding Behavior of Specific Cobalt and Nickel Ion-Binding Peptides Identified by Phage Surface Display. SEPARATIONS 2022. [DOI: 10.3390/separations9110354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In recent years, the application focus of phage surface display (PSD) technology has been extended to the identification of metal ion-selective peptides. In previous studies, two phage clones—a nickel-binding one with the peptide motif CNAKHHPRCGGG and a cobalt-binding one with the peptide motif CTQMLGQLCGGG—were isolated, and their binding ability to metal-loaded NTA agarose beads was investigated. Here, the free cyclic peptides are characterized by UV/VIS spectroscopy with respect to their binding capacity for the respective target ion and in crossover experiments for the other ion by isothermal titration calorimetry (ITC) in different buffer systems. This revealed differences in selectivity and affinity. The cobalt-specific peptide is very sensitive to different buffers; it has a 20-fold higher affinity for cobalt and nickel under suitable conditions. The nickel-specific peptide binds more moderately and robustly in different buffers but only selectively to nickel.
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10
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Odarchenko Y, Kaźmierczak-Bałata A, Bodzenta J, Ferrari E, Soloviev M. AC/DC Thermal Nano-Analyzer Compatible with Bulk Liquid Measurements. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:3799. [PMID: 36364575 PMCID: PMC9655476 DOI: 10.3390/nano12213799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 10/16/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Nanocalorimetry, or thermal nano-analysis, is a powerful tool for fast thermal processing and thermodynamic analysis of materials at the nanoscale. Despite multiple reports of successful applications in the material sciences to study phase transitions in metals and polymers, thermodynamic analysis of biological systems in their natural microenvironment has not been achieved yet. Simply scaling down traditional calorimetric techniques, although beneficial for material sciences, is not always appropriate for biological objects, which cannot be removed out of their native biological environment or be miniaturized to suit instrument limitations. Thermal analysis at micro- or nano-scale immersed in bulk liquid media has not yet been possible. Here, we report an AC/DC modulated thermal nano-analyzer capable of detecting nanogram quantities of material in bulk liquids. The detection principle used in our custom-build instrument utilizes localized heat waves, which under certain conditions confine the measurement area to the surface layer of the sample in the close vicinity of the sensing element. To illustrate the sensitivity and quantitative capabilities of the instrument we used model materials with detectable phase transitions. Here, we report ca. 106 improvement in the thermal analysis sensitivity over a traditional DSC instrument. Interestingly, fundamental thermal properties of the material can be determined independently from heat flow in DC (direct current) mode, by using the AC (alternating current) component of the modulated heat in AC/DC mode. The thermal high-frequency AC modulation mode might be especially useful for investigating thermal transitions on the surface of material, because of the ability to control the depth of penetration of AC-modulated heat and hence the depth of thermal sensing. The high-frequency AC mode might potentially expand the range of applications to the surface analysis of bulk materials or liquid-solid interfaces.
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Affiliation(s)
- Yaroslav Odarchenko
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Anna Kaźmierczak-Bałata
- Institute of Physics, Center for Science and Education, Silesian University of Technology, Konarskiego 22B, 44-100 Gliwice, Poland
| | - Jerzy Bodzenta
- Institute of Physics, Center for Science and Education, Silesian University of Technology, Konarskiego 22B, 44-100 Gliwice, Poland
| | - Enrico Ferrari
- Department of Life Sciences, University of Lincoln, Lincoln LN6 7TS, UK
| | - Mikhail Soloviev
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
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11
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Gadly T, Patro BS, Chakraborty G. Fluorogenic gemcitabine based light up sensor for serum albumin detection in complex biological matrices. Colloids Surf B Biointerfaces 2022; 220:112865. [PMID: 36174489 DOI: 10.1016/j.colsurfb.2022.112865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/11/2022] [Accepted: 09/19/2022] [Indexed: 10/14/2022]
Abstract
Herein we report fluorogenic derivative of gemcitabine (GEM-DNS), synthesized from gemcitabine hydrochloride and dansyl chloride in a single step. Owing to its large stoke shift of ∼200 nm and intriguing photophysical properties, the said dye has been utilized to estimate albumin concentration in complex bio-media such as human urine and blood serum. High sensitivity and selectivity towards albumin make the aforementioned dye a powerful diagnostic tool to detect ailments such as liver cirrhosis, diabetes, hypertension etc.
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Affiliation(s)
- Trilochan Gadly
- Bio-Organic Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Birija S Patro
- Bio-Organic Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Goutam Chakraborty
- Laser & Plasma Technology Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
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12
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Shan T, Huang L, Tay FR, Gu L. Retention of Intrafibrillar Minerals Improves Resin-Dentin Bond Durability. J Dent Res 2022; 101:1490-1498. [PMID: 35708474 DOI: 10.1177/00220345221103137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The concept of extrafibrillar demineralization involves selective removal of apatite crystallites from the extrafibrillar spaces of mineralized dentin without disturbing the intrafibrillar minerals within collagen. This helps avoiding activation of endogenous proteases and enables air-drying of partially demineralized dentin without causing collapse of completely demineralized collagen matrix that adversely affects resin infiltration. The objective of the present study was to evaluate the potential of quaternized carboxymethyl chitosan (QCMC)-based extrafibrillar demineralization in improving resin-dentin bond durability. Isothermal titration calorimetry indicated that QCMC synthesized by quaternization of O-carboxymethyl chitosan had moderate affinity for Ca2+ (binding constant: 8.9 × 104 M-1). Wet and dry bonding with the QCMC-based demineralization produced tensile bond strengths equivalent to the phosphoric acid (H3PO4)-based etch-and-rinse technique. Those bond strengths were maintained after thermocycling. Amide I and PO43- mappings of QCMC-conditioned dentin were performed with atomic force microscope-infrared spectroscopy (AFM-IR). Whereas H3PO4-etched dentin exhibited an extensive reduction in PO43- signals corresponding to apatite depletion, QCMC-conditioned dentin showed scattered dark areas and bright PO43- streak signals. The latter were consistent with areas identified as collagen fibrils in the amide I mapping and were suggestive of the presence of intrafibrillar minerals in QCMC-conditioned dentin. Young's modulus mapping of QCMC-demineralized dentin obtained by AFM-based amplitude modulation-frequency modulation recorded moduli that were the same order of magnitude as those in mineralized dentin and at least 1 order higher than H3PO4-etched dentin. In situ zymography of the gelatinolytic activity within hybrid layers created with QCMC conditioning revealed extremely low signals before and after thermocycling, compared with H3PO4-etched dentin for both wet and dry bonding. Confocal laser scanning microscopy identified the antibacterial potential of QCMC against Streptococcus mutans and Enterococcus faecalis biofilms. Taken together, the QCMC-based demineralization retains intrafibrillar minerals, preserves the elastic modulus of collagen fibrils, reduces endogenous proteolytic activity, and inhibits bacteria biofilms to extend dentin bond durability.
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Affiliation(s)
- T Shan
- Department of Operative Dentistry and Endodontics, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P.R. China
| | - L Huang
- Department of Operative Dentistry and Endodontics, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P.R. China
| | - F R Tay
- Department of Endodontics, The Dental College of Georgia, Augusta University, Augusta, GA, USA
| | - L Gu
- Department of Operative Dentistry and Endodontics, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, P.R. China
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13
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Chen H, Lu Y, Shi S, Zhang Q, Cao X, Sun L, An D, Zhang X, Kong X, Liu J. Design and Development of a New Glucagon-Like Peptide-1 Receptor Agonist to Obtain High Oral Bioavailability. Pharm Res 2022; 39:1891-1906. [PMID: 35698011 DOI: 10.1007/s11095-022-03265-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 04/18/2022] [Indexed: 11/26/2022]
Abstract
PURPOSE Semaglutide is the only oral GLP-1 RA in the market, but oral bioavailability is generally limited in range of 0.4-1%. In this study, a new GLP-1RA named SHR-2042 was developed to gain higher oral bioavailability than semaglutide. METHOD Self-association of SHR-2042, semaglutide and liraglutide were assessed using SEC-MALS. The intestinal perfusion test in SD rats was used to select permeation enhancers (PEs) including SNAC, C10 and LCC. ITC, CD and DLS were used to explore the interaction between SHR-2042 and SNAC. Gastric administrated test in SD rats was used to screen SHR-2042 granules with different SHR-2042/SNAC ratios. The oral bioavailability of SHR-2042 was studied in rats and monkeys. RESULT The designed GLP-1RA, SHR-2042, gives a better solubility and lipophilicity than semaglutide. While it forms a similar oligomer with that of semaglutide. During the selection of PEs, SNAC shows better exposure than the other competing PEs including C10 and LCC. SHR-2042 and SNAC bind quickly and exhibit hydrophobic interaction. SNAC could promote monomerization of SHR-2042 and form micelles to trap the monomerized SHR-2042. The oral bioavailability of SHR-2042 paired with SNAC is 0.041% (1:0, w/w), 0.083% (1:10, w/w), 0.32% (1:30, w/w) and 2.83% (1:60, w/w) in rats. And the oral bioavailability of SHR-2042 matched with SNAC is 3.39% (1:30, w/w) in monkeys, which is over 10 times higher than that of semaglutide. CONCLUSION We believe that the design and development of oral SHR-2042 will provide a new way to design more and more GLP-1RAs with high oral bioavailability in the future.
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Affiliation(s)
- Hao Chen
- School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
- Jiangsu Hengrui Pharmaceuticals Co., Ltd., Lianyungang, 222000, People's Republic of China
| | - Yun Lu
- Jiangsu Hengrui Pharmaceuticals Co., Ltd., Lianyungang, 222000, People's Republic of China
| | - Shuai Shi
- Jiangsu Hengrui Pharmaceuticals Co., Ltd., Lianyungang, 222000, People's Republic of China
| | - Qiang Zhang
- Jiangsu Hengrui Pharmaceuticals Co., Ltd., Lianyungang, 222000, People's Republic of China
| | - Xiaoli Cao
- Jiangsu Hengrui Pharmaceuticals Co., Ltd., Lianyungang, 222000, People's Republic of China
| | - Lei Sun
- Jiangsu Hengrui Pharmaceuticals Co., Ltd., Lianyungang, 222000, People's Republic of China
| | - Dong An
- Jiangsu Hengrui Pharmaceuticals Co., Ltd., Lianyungang, 222000, People's Republic of China
| | - Xiaojie Zhang
- Jiangsu Hengrui Pharmaceuticals Co., Ltd., Lianyungang, 222000, People's Republic of China
| | - Xianglin Kong
- Jiangsu Hengrui Pharmaceuticals Co., Ltd., Lianyungang, 222000, People's Republic of China
| | - Jianping Liu
- School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China.
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14
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Migliore R, Biver T, Barone G, Sgarlata C. Quantitative Analysis of the Interactions of Metal Complexes and Amphiphilic Systems: Calorimetric, Spectroscopic and Theoretical Aspects. Biomolecules 2022; 12:biom12030408. [PMID: 35327600 PMCID: PMC8946196 DOI: 10.3390/biom12030408] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 01/27/2023] Open
Abstract
Metals and metal-based compounds have many implications in biological systems. They are involved in cellular functions, employed in the formation of metal-based drugs and present as pollutants in aqueous systems, with toxic effects for living organisms. Amphiphilic molecules also play important roles in the above bio-related fields as models of membranes, nanocarriers for drug delivery and bioremediating agents. Despite the interest in complex systems involving both metal species and surfactant aggregates, there is still insufficient knowledge regarding the quantitative aspects at the basis of their binding interactions, which are crucial for extensive comprehension of their behavior in solution. Only a few papers have reported quantitative analyses of the thermodynamic, kinetic, speciation and binding features of metal-based compounds and amphiphilic aggregates, and no literature review has yet addressed the quantitative study of these complexes. Here, we summarize and critically discuss the recent contributions to the quantitative investigation of the interactions of metal-based systems with assemblies made of amphiphilic molecules by calorimetric, spectrophotometric and computational techniques, emphasizing the unique picture and parameters that such an analytical approach may provide, to support a deep understanding and beneficial use of these systems for several applications.
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Affiliation(s)
- Rossella Migliore
- Institute of Biomolecular Chemistry, National Research Council, Via Paolo Gaifami 18, 95126 Catania, Italy;
| | - Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy;
| | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, Edificio 17, 90128 Palermo, Italy;
| | - Carmelo Sgarlata
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
- Correspondence:
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15
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Fluorogenic Detection of Human Serum Albumin Using Curcumin-Capped Mesoporous Silica Nanoparticles. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27031133. [PMID: 35164400 PMCID: PMC8838683 DOI: 10.3390/molecules27031133] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 11/16/2022]
Abstract
Mesoporous silica nanoparticles loaded with rhodamine B and capped with curcumin are used for the selective and sensitive fluorogenic detection of human serum albumin (HSA). The sensing mesoporous silica nanoparticles are loaded with rhodamine B, decorated with aminopropyl moieties and capped with curcumin. The nanoparticles selectively release the rhodamine B cargo in the presence of HSA. A limit of detection for HSA of 0.1 mg/mL in PBS (pH 7.4)-acetonitrile 95:5 v/v was found, and the sensing nanoparticles were used to detect HSA in spiked synthetic urine samples.
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16
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Roberts DE, Benton AM, Fabian-Bayola C, Spuches AM, Offenbacher AR. Thermodynamic and biophysical study of fatty acid effector binding to soybean lipoxygenase: implications for allostery driven by helix α2 dynamics. FEBS Lett 2022; 596:350-359. [PMID: 34997975 DOI: 10.1002/1873-3468.14275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/09/2021] [Accepted: 12/20/2021] [Indexed: 11/10/2022]
Abstract
Previous comparative kinetic isotope effects have inferred an allosteric site for fatty acids and their derivatives that modulates substrate selectivity in 15-lipoxygenases. Hydrogen-deuterium exchange also previously revealed regionally defined enhanced protein flexibility, centred at helix α2 - a gate to the substrate entrance. Direct evidence for allosteric binding and a complete understanding of its mechanism remains elusive. In this study, we examine the binding thermodynamics of the fatty acid mimic, oleyl sulfate (OS), with the monomeric model plant 15-LOX, soybean lipoxygenase (SLO), using isothermal titration calorimetry. Dynamic light scattering and differential scanning calorimetry rule out OS-induced oligomerization or structural changes. These data provide evidence that the fatty acid allosteric regulation of SLO is controlled by the dynamics of helix α2.
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Affiliation(s)
| | - Amy M Benton
- Department of Chemistry, East Carolina University, Greenville, NC, USA
| | | | - Anne M Spuches
- Department of Chemistry, East Carolina University, Greenville, NC, USA
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17
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Sun T, Chen Y, Wen Y, Zhu Z, Li M. PremPLI: a machine learning model for predicting the effects of missense mutations on protein-ligand interactions. Commun Biol 2021; 4:1311. [PMID: 34799678 PMCID: PMC8604987 DOI: 10.1038/s42003-021-02826-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023] Open
Abstract
Resistance to small-molecule drugs is the main cause of the failure of therapeutic drugs in clinical practice. Missense mutations altering the binding of ligands to proteins are one of the critical mechanisms that result in genetic disease and drug resistance. Computational methods have made a lot of progress for predicting binding affinity changes and identifying resistance mutations, but their prediction accuracy and speed are still not satisfied and need to be further improved. To address these issues, we introduce a structure-based machine learning method for quantitatively estimating the effects of single mutations on ligand binding affinity changes (named as PremPLI). A comprehensive comparison of the predictive performance of PremPLI with other available methods on two benchmark datasets confirms that our approach performs robustly and presents similar or even higher predictive accuracy than the approaches relying on first-principle statistical mechanics and mixed physics- and knowledge-based potentials while requires much less computational resources. PremPLI can be used for guiding the design of ligand-binding proteins, identifying and understanding disease driver mutations, and finding potential resistance mutations for different drugs. PremPLI is freely available at https://lilab.jysw.suda.edu.cn/research/PremPLI/ and allows to do large-scale mutational scanning. Sun et al. present PremPLI, a machine learning approach and web tool to predict how missense mutations in a drug’s target protein will affect the drug’s binding affinity. PremPLI can be applied to identify drug resistance mechanisms in cancer cells and microorganisms and develop drugs to combat drug resistance.
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Affiliation(s)
- Tingting Sun
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, 215123, Suzhou, China
| | - Yuting Chen
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, 215123, Suzhou, China
| | - Yuhao Wen
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, 215123, Suzhou, China
| | - Zefeng Zhu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, 215123, Suzhou, China
| | - Minghui Li
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, 215123, Suzhou, China.
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18
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Wang J, Yu X, Jia R, Liu R, Zong W. An in vitro and in silico study to explore the response of catalase to 4-chlorophenol and their interacting mechanisms. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Liu C, Seeram NP, Ma H. Small molecule inhibitors against PD-1/PD-L1 immune checkpoints and current methodologies for their development: a review. Cancer Cell Int 2021; 21:239. [PMID: 33906641 PMCID: PMC8077906 DOI: 10.1186/s12935-021-01946-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/19/2021] [Indexed: 12/12/2022] Open
Abstract
Programmed death-1/programmed death ligand-1 (PD-1/PD-L1) based immunotherapy is a revolutionary cancer therapy with great clinical success. The majority of clinically used PD-1/PD-L1 inhibitors are monoclonal antibodies but their applications are limited due to their poor oral bioavailability and immune-related adverse effects (irAEs). In contrast, several small molecule inhibitors against PD-1/PD-L1 immune checkpoints show promising blockage effects on PD-1/PD-L1 interactions without irAEs. However, proper analytical methods and bioassays are required to effectively screen small molecule derived PD-1/PD-L1 inhibitors. Herein, we summarize the biophysical and biochemical assays currently employed for the measurements of binding capacities, molecular interactions, and blocking effects of small molecule inhibitors on PD-1/PD-L1. In addition, the discovery of natural products based PD-1/PD-L1 antagonists utilizing these screening assays are reviewed. Potential pitfalls for obtaining false leading compounds as PD-1/PD-L1 inhibitors by using certain binding bioassays are also discussed in this review.
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Affiliation(s)
- Chang Liu
- Bioactive Botanical Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Avedisian Hall Lab 440, 7 Greenhouse Road, Kingston, RI, 02881, USA.
| | - Navindra P Seeram
- Bioactive Botanical Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Avedisian Hall Lab 440, 7 Greenhouse Road, Kingston, RI, 02881, USA
| | - Hang Ma
- Bioactive Botanical Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Avedisian Hall Lab 440, 7 Greenhouse Road, Kingston, RI, 02881, USA.
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20
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Anderson SE, Longbotham JE, O'Kane PT, Ugur FS, Fujimori DG, Mrksich M. Exploring the Ligand Preferences of the PHD1 Domain of Histone Demethylase KDM5A Reveals Tolerance for Modifications of the Q5 Residue of Histone 3. ACS Chem Biol 2021; 16:205-213. [PMID: 33314922 PMCID: PMC8168426 DOI: 10.1021/acschembio.0c00891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Understanding the ligand preferences of epigenetic reader domains enables identification of modification states of chromatin with which these domains associate and can yield insight into recruitment and catalysis of chromatin-acting complexes. However, thorough exploration of the ligand preferences of reader domains is hindered by the limitations of traditional protein-ligand binding assays. Here, we evaluate the binding preferences of the PHD1 domain of histone demethylase KDM5A using the protein interaction by SAMDI (PI-SAMDI) assay, which measures protein-ligand binding in a high-throughput and sensitive manner via binding-induced enhancement in the activity of a reporter enzyme, in combination with fluorescence polarization. The PI-SAMDI assay was validated by confirming its ability to accurately profile the relative binding affinity of a set of well-characterized histone 3 (H3) ligands of PHD1. The assay was then used to assess the affinity of PHD1 for 361 H3 mutant ligands, a select number of which were further characterized by fluorescence polarization. Together, these experiments revealed PHD1's tolerance for H3Q5 mutations, including an unexpected tolerance for aromatic residues in this position. Motivated by this finding, we further demonstrate a high-affinity interaction between PHD1 and recently identified Q5-serotonylated H3. This work yields interesting insights into permissible PHD1-H3 interactions and demonstrates the value of interfacing PI-SAMDI and fluorescence polarization in investigations of protein-ligand binding.
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Affiliation(s)
- Sarah E Anderson
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - James E Longbotham
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Patrick T O'Kane
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Fatima S Ugur
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, California 94158, United States
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, United States
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, California 94158, United States
| | - Milan Mrksich
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Cell and Developmental Biology, Northwestern University, Evanston, Illinois 60208, United States
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21
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Ge X, Chen L, Li D, Liu R, Ge G. Estimation of non-constant variance in isothermal titration calorimetry using an ITC measurement model. PLoS One 2020; 15:e0244739. [PMID: 33378411 PMCID: PMC7773272 DOI: 10.1371/journal.pone.0244739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 12/15/2020] [Indexed: 11/30/2022] Open
Abstract
Isothermal titration calorimetry (ITC) is the gold standard for accurate measurement of thermodynamic parameters in solution reactions. In the data processing of ITC, the non-constant variance of the heat requires special consideration. The variance function approach has been successfully applied in previous studies, but is found to fail under certain conditions in this work. Here, an explicit ITC measurement model consisting of main thermal effects and error components has been proposed to quantitatively evaluate and predict the non-constant variance of the heat data under various conditions. Monte Carlo simulation shows that the ITC measurement model provides higher accuracy and flexibility than variance function in high c-value reactions or with additional error components, for example, originated from the fluctuation of the concentrations or other properties of the solutions. The experimental design of basic error evaluation is optimized accordingly and verified by both Monte Carlo simulation and experiments. An easy-to-run Python source code is provided to illustrate the establishment of the ITC measurement model and the estimation of heat variances. The accurate and reliable non-constant variance of heat is helpful to the application of weighted least squares regression, the proper evaluation or selection of the reaction model.
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Affiliation(s)
- Xiujie Ge
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Lan Chen
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, P. R. China
| | - Dexing Li
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, P. R. China
- * E-mail: (DL); (GG)
| | - Renxiao Liu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, P. R. China
| | - Guanglu Ge
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, P. R. China
- * E-mail: (DL); (GG)
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22
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Konar M, Sahoo H. Exploring the chemistry behind protein-glycosaminoglycan conjugate: A steady-state and kinetic spectroscopy based approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 242:118726. [PMID: 32745937 DOI: 10.1016/j.saa.2020.118726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
The impact of glycosaminoglycan (chondroitin sulphate, CS) on bone morphogenetic protein - 2 (BMP - 2) structure, stability (thermal and chemical), association kinetics and conformation was monitored by multiple spectroscopic techniques (UV-Visible, fluorescence and circular dichroism). The absorbance in peptide region and fluorescence intensity of BMP - 2 was quenched in presence of CS; thus, confirming the formation of a ground-state complex. As there was an increase in Stern-Volmer constant observed as a function of temperature, idea of dynamic quenching was established. However, the negligible changes in lifetime indicated static quenching; thus, making the process a combination of static-dynamic quenching. Basically, the protein - glycan interaction was driven by entropy of the system and mediated by hydrophobic interactions. Secondary structure (CD spectroscopy) of native protein was significantly affected (intensity became more negative) in presence of CS, thus, introducing more compactness in the protein. CS infused thermal and chemical stability into BMP - 2 via alteration in its conformation. The rate of association was inversely proportional to concentration of quencher (CS), which confirmed the correlation between large size (~ 5 times the size of protein) and structural complexity of CS with fewer binding sites present in BMP - 2. The rate of association in presence of urea, suggested a decrease in association rate as a function of urea concentration for 15 μM CS. Experimental evidences suggested an interaction between protein and glycan mediated by hydrophobic interactions, which deciphers structural, thermal and chemical stability into protein.
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Affiliation(s)
- Monidipa Konar
- Biophysical Chemistry Lab, Department of Chemistry, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| | - Harekrushna Sahoo
- Biophysical Chemistry Lab, Department of Chemistry, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India.
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23
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Pearlstein RA, Wan H, Aravamuthan V. Toward in vivo relevant drug design. Drug Discov Today 2020; 26:637-650. [PMID: 33132106 DOI: 10.1016/j.drudis.2020.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 09/16/2020] [Accepted: 10/15/2020] [Indexed: 11/28/2022]
Abstract
Current early and preclinical drug discovery are rooted in decades-old empirical principles describing structure-free energy and structure-function relationships under equilibrium conditions that frequently break down under in vivo conditions. Improved prediction of efficacy and toxicity depends on a paradigm shift to in vivo-relevant principles describing the true nonequilibrium/nonlinear dynamic (NLD) nature of cellular systems. Here, we outline a holistic, in vivo-relevant first principles theory ('Biodynamics'), in which cellular function/dysfunction, and pharmaco-/toxicodynamic effects are considered as emergent behaviors of multimolecular systems powered by covalent and noncovalent free energy sources. The reduction to practice of Biodynamics theory consists of in silico simulations performed at the atomistic and molecular systems levels, versus empirical models fit to in vitro data under the classical paradigm.
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Affiliation(s)
- Robert A Pearlstein
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Hongbin Wan
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Vibhas Aravamuthan
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
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24
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Wang Y, Wang G, Moitessier N, Mittermaier AK. Enzyme Kinetics by Isothermal Titration Calorimetry: Allostery, Inhibition, and Dynamics. Front Mol Biosci 2020; 7:583826. [PMID: 33195429 PMCID: PMC7604385 DOI: 10.3389/fmolb.2020.583826] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/11/2020] [Indexed: 12/14/2022] Open
Abstract
Isothermal titration calorimetry (ITC) involves accurately measuring the heat that is released or absorbed in real time when one solution is titrated into another. This technique is usually used to measure the thermodynamics of binding reactions. However, there is mounting interest in using it to measure reaction kinetics, particularly enzymatic catalysis. This application of ITC has been steadily growing for the past two decades, and the method is proving to be sensitive, generally applicable, and capable of providing information on enzyme activity that is difficult to obtain using traditional biochemical assays. This review aims to give a broad overview of the use of ITC to measure enzyme kinetics. It describes several different classes of ITC experiment, their strengths and weaknesses, and recent methodological advancements. A summary of applications in the literature is given and several examples where ITC has been used to investigate challenging aspects of enzyme behavior are presented in more detail. These include examples of allostery, where small-molecule binding outside the active site modulates activity. We describe the use of ITC to measure the strength, mode (i.e., competitive, uncompetitive, or mixed), and association and dissociation kinetics of enzyme inhibitors. Further, we provide examples of ITC applied to complex, heterogeneous mixtures, such as insoluble substrates and live cells. These studies exemplify the wide range of problems where ITC can provide answers, and illustrate the versatility of the technique and potential for future development and applications.
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Affiliation(s)
- Yun Wang
- Department of Chemistry, McGill University, Montreal, QC, Canada
| | - Guanyu Wang
- Department of Chemistry, McGill University, Montreal, QC, Canada
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Khan MT, Ali S, Zeb MT, Kaushik AC, Malik SI, Wei DQ. Gibbs Free Energy Calculation of Mutation in PncA and RpsA Associated With Pyrazinamide Resistance. Front Mol Biosci 2020; 7:52. [PMID: 32328498 PMCID: PMC7160322 DOI: 10.3389/fmolb.2020.00052] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/16/2020] [Indexed: 12/16/2022] Open
Abstract
A central approach for better understanding the forces involved in maintaining protein structures is to investigate the protein folding and thermodynamic properties. The effect of the folding process is often disturbed in mutated states. To explore the dynamic properties behind mutations, molecular dynamic (MD) simulations have been widely performed, especially in unveiling the mechanism of drug failure behind mutation. When comparing wild type (WT) and mutants (MTs), the structural changes along with solvation free energy (SFE), and Gibbs free energy (GFE) are calculated after the MD simulation, to measure the effect of mutations on protein structure. Pyrazinamide (PZA) is one of the first-line drugs, effective against latent Mycobacterium tuberculosis isolates, affecting the global TB control program 2030. Resistance to this drug emerges due to mutations in pncA and rpsA genes, encoding pyrazinamidase (PZase) and ribosomal protein S1 (RpsA) respectively. The question of how the GFE may be a measure of PZase and RpsA stabilities, has been addressed in the current review. The GFE and SFE of MTs have been compared with WT, which were already found to be PZA-resistant. WT structures attained a more stable state in comparison with MTs. The physiological effect of a mutation in PZase and RpsA may be due to the difference in energies. This difference between WT and MTs, depicted through GFE plots, might be useful in predicting the stability and PZA-resistance behind mutation. This study provides useful information for better management of drug resistance, to control the global TB problem.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Sajid Ali
- Department of Microbiology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | | | - Aman Chandra Kaushik
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, China
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Archer WR, Fiorito A, Heinz-Kunert SL, MacNicol PL, Winn SA, Schulz MD. Synthesis and Rare-Earth-Element Chelation Properties of Linear Poly(ethylenimine methylenephosphonate). Macromolecules 2020. [DOI: 10.1021/acs.macromol.9b02472] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- William R. Archer
- Department of Chemistry, Macromolecules Innovation Institute (MII), Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Agustin Fiorito
- Department of Chemistry, Macromolecules Innovation Institute (MII), Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Sherrie L. Heinz-Kunert
- Department of Chemistry, Macromolecules Innovation Institute (MII), Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Piper L. MacNicol
- Department of Chemistry, Macromolecules Innovation Institute (MII), Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Samantha A. Winn
- Department of Chemistry, Macromolecules Innovation Institute (MII), Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Michael D. Schulz
- Department of Chemistry, Macromolecules Innovation Institute (MII), Virginia Tech, Blacksburg, Virginia 24061, United States
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Wang DD, Ou-Yang L, Xie H, Zhu M, Yan H. Predicting the impacts of mutations on protein-ligand binding affinity based on molecular dynamics simulations and machine learning methods. Comput Struct Biotechnol J 2020; 18:439-454. [PMID: 32153730 PMCID: PMC7052406 DOI: 10.1016/j.csbj.2020.02.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 01/31/2020] [Accepted: 02/11/2020] [Indexed: 01/19/2023] Open
Abstract
Purpose Mutation-induced variation of protein-ligand binding affinity is the key to many genetic diseases and the emergence of drug resistance, and therefore predicting such mutation impacts is of great importance. In this work, we aim to predict the mutation impacts on protein-ligand binding affinity using efficient structure-based, computational methods. Methods Relying on consolidated databases of experimentally determined data we characterize the affinity change upon mutation based on a number of local geometrical features and monitor such feature differences upon mutation during molecular dynamics (MD) simulations. The differences are quantified according to average difference, trajectory-wise distance or time-vary differences. Machine-learning methods are employed to predict the mutation impacts using the resulting conventional or time-series features. Predictions based on estimation of energy and based on investigation of molecular descriptors were conducted as benchmarks. Results Our method (machine-learning techniques using time-series features) outperformed the benchmark methods, especially in terms of the balanced F1 score. Particularly, deep-learning models led to the best prediction performance with distinct improvements in balanced F1 score and a sustained accuracy. Conclusion Our work highlights the effectiveness of the characterization of affinity change upon mutations. Furthermore, deep-learning techniques are well designed for handling the extracted time-series features. This study can lead to a deeper understanding of mutation-induced diseases and resistance, and further guide the development of innovative drug design.
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Key Words
- CNN, convolutional neural network
- Deep learning
- HMM, hidden Markov model
- LSTM, long short-term memory
- Local geometrical features
- MD, molecular dynamics
- MM/GBSA, molecular mechanics/generalized born surface area
- MM/PBSA, molecular mechanics/Poisson-Boltzmann surface area
- Missense mutation
- Molecular dynamics (MD) simulations
- Mutation impact
- Protein-ligand binding affinity
- RF, random forest
- RMSD, root-mean-square deviation
- RNN, recurrent neural network
- SASA, solvent accessible surface area
- Time series features
- WTP, wildtype protein
- aacomp, amino acid composition descriptors
- const, constitutional descriptors
- ctd, composition transition and distribution descriptors
- kappa, Kappa shape indices
- paacomp, type 1 pseudo amino acid composition descriptors
- top, topological descriptors
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Affiliation(s)
- Debby D. Wang
- Institute of Medical Information Engineering, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, 516 Jungong Rd, Shanghai 200093, China
- Corresponding author at: Institute of Medical Information Engineering, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, 516 Jungong Rd, Shanghai 200093, China.
| | - Le Ou-Yang
- Guangdong Key Laboratory of Intelligent Information Processing and Shenzhen Key Laboratory of Media Security, College of Electronics and Information Engineering, Shenzhen University, 3688 Nanhai Ave, Shenzhen 518060, China
- Corresponding author at: Institute of Medical Information Engineering, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, 516 Jungong Rd, Shanghai 200093, China.
| | - Haoran Xie
- Department of Computing and Decision Sciences, Lingnan University, 8 Castle Peak Rd, Tuen Mun, Hong Kong
| | - Mengxu Zhu
- Department of Electrical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Hong Yan
- Department of Electrical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
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Tu Y, Yu Y, Zhou Z, Xie S, Yao B, Guan S, Situ B, Liu Y, Kwok RTK, Lam JWY, Chen S, Huang X, Zeng Z, Tang BZ. Specific and Quantitative Detection of Albumin in Biological Fluids by Tetrazolate-Functionalized Water-Soluble AIEgens. ACS APPLIED MATERIALS & INTERFACES 2019; 11:29619-29629. [PMID: 31340641 DOI: 10.1021/acsami.9b10359] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The analysis of albumin has clinical significance in diagnostic tests and obvious value to research studies on the albumin-mediated drug delivery and therapeutics. The present immunoassay, instrumental techniques, and colorimetric methods for albumin detection are either expensive, troublesome, or insensitive. Herein, a class of water-soluble tetrazolate-functionalized derivatives with aggregation-induced emission (AIE) characteristics is introduced as novel fluorescent probes for albumin detection. They can be selectively lighted up by site-specific binding with albumin. The resulting albumin fluorescent assay exhibits a low detection limit (0.21 nM), high robustness in aqueous buffer (pH = 6-9), and a broad tunable linear dynamic range (0.02-3000 mg/L) for quantification. The tetrazolate functionality endows the probes with a superior water solubility (>0.01 M) and a high binding affinity to albumin (KD = 0.25 μM). To explore the detection mechanism, three unique polar binding sites on albumin are computationally identified, where the multivalent tetrazolate-lysine interactions contribute to the tight binding and restriction of the molecular motion of the AIE probes. The key role of lysine residues is verified by the detection of poly-l-lysine. Moreover, we applied the fluorogenic method to quantify urinary albumin in clinical samples and found it a feasible and practical strategy for albumin analysis in complex biological fluids.
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Affiliation(s)
- Yujie Tu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , China
| | | | - Zhibiao Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , China
| | - Sheng Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , China
| | | | - Shujuan Guan
- Department of Laboratory Medicine, Nanfang Hospital , Southern Medical University , Guangzhou 510515 , China
| | - Bo Situ
- Department of Laboratory Medicine, Nanfang Hospital , Southern Medical University , Guangzhou 510515 , China
| | | | | | | | - Sijie Chen
- Ming Wai Lau Center for Reparative Medicine , Karolinska Institutet , Hong Kong 999077 , China
| | | | - Zebing Zeng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , China
| | - Ben Zhong Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , China
- State Key Laboratory of Luminescent Materials and Devices, Center for Aggregation-Induced Emission, (Guangzhou International Campus) , South China University of Technology , Guangzhou 510640 , China
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Witkowska D, Rowińska-Żyrek M. Biophysical approaches for the study of metal-protein interactions. J Inorg Biochem 2019; 199:110783. [PMID: 31349072 DOI: 10.1016/j.jinorgbio.2019.110783] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions play important roles for a variety of cell functions, often involving metal ions; in fact, metal-ion binding mediates and regulates the activity of a wide range of biomolecules. Enlightening all of the specific features of metal-protein and metal-mediated protein-protein interactions can be a very challenging task; a detailed knowledge of the thermodynamic and spectroscopic parameters and the structural changes of the protein is normally required. For this purpose, many experimental techniques are employed, embracing all fields of Analytical and Bioinorganic Chemistry. In addition, the use of peptide models, reproducing the primary sequence of the metal-binding sites, is also proved to be useful. In this paper, a review of the most useful techniques for studying ligand-protein interactions with a special emphasis on metal-protein interactions is provided, with a critical summary of their strengths and limitations.
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Affiliation(s)
- Danuta Witkowska
- Public Higher Medical Professional School in Opole, Katowicka 68, 45060 Opole, Poland.
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Zheng Q, Ruan X, Tian Y, Hu J, Wan N, Lu W, Xu X, Wang G, Hao H, Ye H. Ligand-protein target screening from cell matrices using reactive desorption electrospray ionization-mass spectrometry via a native-denatured exchange approach. Analyst 2019; 144:512-520. [PMID: 30489587 DOI: 10.1039/c8an01708e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Native mass spectrometry has been recognized as a powerful tool for probing interactions between small molecules, such as drugs and natural products, and target proteins. However, the presence of heterogeneous proteins and metabolites in real biological systems can alter the conformations of target proteins or compete with candidate ligands, thus necessitating a method for measuring binding stoichiometries in matrices aside from the extensively used pure/recombinant protein systems. Furthermore, some small molecule-protein interactions have a transient and low-affinity nature and thus can be mis-assigned as nonspecific binding complexes that are often formed during the native ESI process. A native-denatured exchange (NDX) approach was recently developed using a reactive desorption electrospray ionization-mass spectrometer (DESI-MS) setup to screen specific interacting partners. The method works by gradually increasing the composition of denaturing solvents contained in the DESI spray and thus conferring a switch from a native to denatured ionization environment. This change impairs three-dimensional structures of target proteins and disrupts specific ligand-protein interactions, leading to decreased holo/apo ratios. In contrast, ligand-protein complexes exhibiting different trends are assigned as nonspecific interactions. Herein, we applied the NDX approach to probe specific ligand-protein interactions in biological matrices. We first used mixtures of model ligands and proteins to examine the use of reactive DESI-MS in recognizing ligand-target binding in mixtures. Subsequently, we used the NDX approach to analyze binding affinity curves of ligands to target proteins spiked in cell lysates with the aid of size exclusion chromatography and demonstrated its use in probing specific ligand-protein interactions from cell matrices.
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Affiliation(s)
- Qiuling Zheng
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, College of Pharmacy, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China.
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Downregulation of SNX27 expression does not exacerbate amyloidogenesis in the APP/PS1 Alzheimer's disease mouse model. Neurobiol Aging 2019; 77:144-153. [DOI: 10.1016/j.neurobiolaging.2019.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/01/2019] [Accepted: 01/13/2019] [Indexed: 12/20/2022]
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Guo JM, Makvandi P, Wei CC, Chen JH, Xu HK, Breschi L, Pashley DH, Huang C, Niu LN, Tay FR. Polymer conjugation optimizes EDTA as a calcium-chelating agent that exclusively removes extrafibrillar minerals from mineralized collagen. Acta Biomater 2019; 90:424-440. [PMID: 30953801 DOI: 10.1016/j.actbio.2019.04.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 01/22/2023]
Abstract
During development of mineralized collagenous tissues, intrafibrillar mineralization is achieved by preventing mineralization precursor inhibitors that are larger than 40 kDa from entering the collagen fibrils. Such a property is incorporated in the design of a calcium chelator for dentin bonding in the etch-and-rinse technique that selectively demineralizes extrafibrillar apatite while leaving the intrafibrillar minerals intact. This strategy prevents complete demineralization of collagen fibrils, avoids collapse of collagen that blocks resin infiltration after air-drying, and protects the completely demineralized fibrils from bacteria colonization and degradation by endogenous proteases after resin bonding. In the present study, a water-soluble glycol chitosan-EDTA (GCE) conditioner was synthesized by conjugation of EDTA, an effective calcium chelator, to high molecular weight glycol chitosan, which exhibits weak chelation property. The GCE conjugate was purified, characterized by FTIR, 1H NMR, isothermal titration calorimetry and ICP-AES, and subjected to size exclusion dialysis to recover molecules that are >40 kDa. The optimal concentration and application time for etching dentin were determined by bond strength testing to ensure that the dentin bonding results were comparable to phosphoric acid etching, and maintained equivalent bond strength after air-drying of the conditioned collagen matrix. Extrafibrillar demineralization was validated with transmission electron microscopy. Inhibition of endogenous dentin proteases was confirmed using in-situ zymography. The water-soluble GCE dentin conditioner was non-cytotoxic and possessed antibacterial activities against planktonic and single-species biofilms, supporting its ongoing development as a dentin conditioner with air-drying, anti-proteolytic and antibacterial properties to enhance the durability of bonds created using the etch-and-rinse bonding technique. STATEMENT OF SIGNIFICANCE: The current state-of-the-art techniques for filling decayed teeth with plastic tooth-colored materials require conditioning the mineralized, biofilm-covered, decayed dentin with acids or acid resin monomers to create a surface layer of completely- or partially-demineralized collagen matrix for the infiltration of adhesive resin monomers. Nevertheless, fillings prepared using these strategies are not as durable as consumers have anticipated. Conjugation of polymeric glycol chitosan with EDTA produces a new conditioner for dentin bonding that demineralizes only extrafibrillar dentin, reduces endogenous protease activities and kills biofilm bacteria. The high molecular weight glycol chitosan-EDTA is non-cytotoxic to the key regenerative players within the dentin-pulp complex. This advance permits dry bonding and the use of hydrophobic resins.
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Šolínová V, Žáková L, Jiráček J, Kašička V. Pressure assisted partial filling affinity capillary electrophoresis employed for determination of binding constants of human insulin hexamer complexes with serotonin, dopamine, arginine, and phenol. Anal Chim Acta 2019; 1052:170-178. [DOI: 10.1016/j.aca.2018.11.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/10/2018] [Accepted: 11/12/2018] [Indexed: 11/30/2022]
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Yasmeen S, Riyazuddeen, Khatun S, Abul Qais F. Characterization of interactions between cromolyn sodium and bovine serum albumin by spectroscopic, calorimetric and computational methods. J Biomol Struct Dyn 2019; 38:722-732. [DOI: 10.1080/07391102.2019.1586588] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Shama Yasmeen
- Department of Chemistry, Aligarh Muslim University, Aligarh, India
| | - Riyazuddeen
- Department of Chemistry, Aligarh Muslim University, Aligarh, India
| | - Samima Khatun
- Department of Chemistry, Aligarh Muslim University, Aligarh, India
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, India
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Petit JD, Immel F, Lins L, Bayer EM. Lipids or Proteins: Who Is Leading the Dance at Membrane Contact Sites? FRONTIERS IN PLANT SCIENCE 2019; 10:198. [PMID: 30846999 PMCID: PMC6393330 DOI: 10.3389/fpls.2019.00198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/05/2019] [Indexed: 05/19/2023]
Abstract
Understanding the mode of action of membrane contact sites (MCSs) across eukaryotic organisms at the near-atomic level to infer function at the cellular and tissue levels is a challenge scientists are currently facing. These peculiar systems dedicated to inter-organellar communication are perfect examples of cellular processes where the interplay between lipids and proteins is critical. In this mini review, we underline the link between membrane lipid environment, the recruitment of proteins at specialized membrane domains and the function of MCSs. More precisely, we want to give insights on the crucial role of lipids in defining the specificity of plant endoplasmic reticulum (ER)-plasma membrane (PM) MCSs and we further propose approaches to study them at multiple scales. Our goal is not so much to go into detailed description of MCSs, as there are numerous focused reviews on the subject, but rather try to pinpoint the critical elements defining those structures and give an original point of view by considering the subject from a near-atomic angle with a focus on lipids. We review current knowledge as to how lipids can define MCS territories, play a role in the recruitment and function of the MCS-associated proteins and in turn, how the lipid environment can be modified by proteins.
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Affiliation(s)
- Jules D. Petit
- UMR5200 CNRS, Laboratory of Membrane Biogenesis, University of Bordeaux, Villenave d’Ornon, France
- Laboratoire de Biophysique Moléculaire aux Interfaces, TERRA Research Centre, GX ABT, Université de Liège, Liège, Belgium
| | - Françoise Immel
- UMR5200 CNRS, Laboratory of Membrane Biogenesis, University of Bordeaux, Villenave d’Ornon, France
| | - Laurence Lins
- Laboratoire de Biophysique Moléculaire aux Interfaces, TERRA Research Centre, GX ABT, Université de Liège, Liège, Belgium
| | - Emmanuelle M. Bayer
- UMR5200 CNRS, Laboratory of Membrane Biogenesis, University of Bordeaux, Villenave d’Ornon, France
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Klebe G. Broad-scale analysis of thermodynamic signatures in medicinal chemistry: are enthalpy-favored binders the better development option? Drug Discov Today 2019; 24:943-948. [PMID: 30708050 DOI: 10.1016/j.drudis.2019.01.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/18/2019] [Accepted: 01/24/2019] [Indexed: 12/30/2022]
Abstract
Thermodynamic profiles of ligand binding, particularly enthalpically favored binding signatures, have been suggested as a criterion to support the decision-making process around which compounds to select for further optimization in drug development. The concept was enthusiastically taken up, but turned out to be too superficial, either because many aspects determining thermodynamic profiles are insufficiently appreciated or because it is difficult to compare such data on a global scale. The impact of water, changes in protonation states, along with buffer dependencies and incompatible measurement conditions that are far from standard conditions hamper such broad-scale comparisons. However, thermodynamic signatures can make us aware of the impact of these aspects and provide important hints for improving our understanding of the binding process and defining criteria for drug optimization.
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Affiliation(s)
- Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany.
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Liu Z, Fan Y, Wang Y. Selective separation of heavy metal ions from dilute aqueous solutions by foams and micelles of surfactants. SOFT MATTER 2018; 14:9830-9837. [PMID: 30484809 DOI: 10.1039/c8sm02036a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Traditional metal ion separation by surfactant foams is dependent on the interaction difference of various metal ions with surfactant monomers rather than surfactant aggregates, because the binding of metal ions with surfactant aggregates retains the metal ions in bulk solution. This kind of separation method is only effective for the metal ions with obvious differences in valence, size or coordination ability. The present study proposes a novel separation method based on the binding affinity difference of metal ions with micelles and monomers of two surfactants to selectively separate multivalent ions Cr3+, Ni2+ and Cu2+ from their dilute mixed aqueous solution. The two surfactants are single-chain surfactant sodium dodecyl sulfate (SDS) and gemini surfactant 1,3-bis(N-dodecyl-N-propanesulfonate sodium)-propane (C12C3C12(SO3)2), which show negligible synergism because they are both negatively charged and hold a significantly different self-assembling ability, thus allowing the coexistence of SDS/C12C3C12(SO3)2 micelles with SDS monomers. At first, Cr3+ ions were separated from Cu2+ and Ni2+ ions by the foam generated by the SDS monomers due to more intensive electrostatic interaction of Cr3+ ions with the SDS monomers. Afterwards Ni2+ ions were separated from Cu2+ ions by utilizing the high binding affinity of Cu2+ with the SDS/C12C3C12(SO3)2 micelles in the bulk solution and Ni2+ with the SDS monomers in the foam. This work has proved that micelles can assist the selective separation of "twin-like" metal ions Ni2+ and Cu2+ when the concentrations of monomers and micelles are properly adjusted.
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Affiliation(s)
- Zhang Liu
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
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Zhang Z, Liu J. An engineered one-site aptamer with higher sensitivity for label-free detection of adenosine on graphene oxide. CAN J CHEM 2018. [DOI: 10.1139/cjc-2017-0601] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The 27-nucleotide DNA aptamer for adenosine and ATP, originally selected by the Szostak lab in 1995, has been a very popular model system for biosensor development. This unique aptamer has two target binding sites, and we recently showed that it is possible to remove either site while the other one still retains binding. From an analytical perspective, tuning the number of binding sites has important implications in modulating sensitivity of the resulting biosensors. In this work, we report that the engineered one-site aptamer showed excellent signaling properties with a 2.6-fold stronger signal intensity and also a 4.2-fold increased detection limit compared with the wild-type two-site aptamer. The aptamer has a hairpin structure, and the length of the hairpin stem was systematically varied for the one-site aptamers. Isothermal titration calorimetry and a label-free fluorescence signaling method with graphene oxide and SYBR Green I were respectively used to evaluate binding and sensor performance. Although longer stemmed aptamers produced better adenosine binding affinity, the signaling was quite independent of the stem length as long as more than three base pairs were left. This was explained by the higher affinity of binding to GO by the longer aptamers, cancelling out the higher affinity for adenosine binding. This work further confirms the analytical applications of such one-site adenosine aptamers, which are potentially useful for improved ATP imaging and for developing new biosensors.
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Affiliation(s)
- Zijie Zhang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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Su H, Xu Y. Application of ITC-Based Characterization of Thermodynamic and Kinetic Association of Ligands With Proteins in Drug Design. Front Pharmacol 2018; 9:1133. [PMID: 30364164 PMCID: PMC6193069 DOI: 10.3389/fphar.2018.01133] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/18/2018] [Indexed: 01/20/2023] Open
Abstract
A comprehensive characterization of the thermodynamic and kinetic profiling of ligands binding to a given target protein is crucial for the hit selection as well as the hit-to-lead-to-drug evolution. Isothermal titration calorimetry (ITC), widely known as an invaluable tool to measure the thermodynamic data, has recently found its way to determine the binding kinetics too. The extensive application of ITC in measurement of both thermodynamic and kinetic data manifests unique roles of ITC in drug discovery and development. This mini-review concentrates on elaborating how to gain the thermodynamic and kinetic data using ITC, highlighting the importance of these data in lead discovery and optimization, and intends to provide an overview of the technical and conceptual advances that offer unprecedented access to protein–ligand recognition by ITC measurement.
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Affiliation(s)
- Haixia Su
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
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40
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Sprakel LMJ, Schuur B. Thermal Activity in Affinity Separation Techniques Such as Liquid-Liquid Extraction Analyzed by Isothermal Titration Calorimetry and Accuracy Analysis of the Technique in the Molar Concentration Domain. Ind Eng Chem Res 2018; 57:12574-12582. [PMID: 30270979 PMCID: PMC6156095 DOI: 10.1021/acs.iecr.8b03066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/16/2018] [Accepted: 08/22/2018] [Indexed: 11/30/2022]
Abstract
![]()
The applicability and accuracy of
isothermal titration calorimetry
(ITC) to investigate intermolecular interactions in a high concentration
domain applicable to liquid–liquid extraction (LLX) was studied
for acid–base interactions. More accurate fits can be obtained
using a sequential binding mechanism compared to a single reaction
model, at the risk of finding a local minimum. Experiments with 0.24
M tri-n-octylamine (TOA) resulted in a residue of
fit of 4.3% for the single reaction model, with a standard deviation
σ of 1.6% in the stoichiometry parameter n,
12% in the complexation constant Kn,1, and 2.5% in the enthalpy ΔHn,1. For the sequential model, σ was
higher: 11% in K1,1, 26% in Kn+1,1, and 12% in ΔHn+1,1. This study clearly showed that,
at higher concentrations (order of moles per liter), accurate parameter
estimation is possible and parameter values are concentration dependent.
It is thus important to do ITC at the application concentration.
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Affiliation(s)
- Lisette M J Sprakel
- Sustainable Process Technology Group, Faculty of Science and Technology, University of Twente, Drienerlolaan 5, Meander 221, 7522 NB Enschede, The Netherlands
| | - Boelo Schuur
- Sustainable Process Technology Group, Faculty of Science and Technology, University of Twente, Drienerlolaan 5, Meander 221, 7522 NB Enschede, The Netherlands
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41
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Ostromohov N, Huber D, Bercovici M, Kaigala GV. Real-Time Monitoring of Fluorescence in Situ Hybridization Kinetics. Anal Chem 2018; 90:11470-11477. [DOI: 10.1021/acs.analchem.8b02630] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Nadya Ostromohov
- IBM Research—Zurich, Säumerstrasse 4, 8803 Rüschlikon, Zurich, Switzerland
- Faculty of Mechanical Engineering, Technion—Israel Institute of Technology, Haifa 3200003, Israel
| | - Deborah Huber
- IBM Research—Zurich, Säumerstrasse 4, 8803 Rüschlikon, Zurich, Switzerland
| | - Moran Bercovici
- Faculty of Mechanical Engineering, Technion—Israel Institute of Technology, Haifa 3200003, Israel
| | - Govind V. Kaigala
- IBM Research—Zurich, Säumerstrasse 4, 8803 Rüschlikon, Zurich, Switzerland
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42
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Bharmoria P, Hisamitsu S, Nagatomi H, Ogawa T, Morikawa MA, Yanai N, Kimizuka N. Simple and Versatile Platform for Air-Tolerant Photon Upconverting Hydrogels by Biopolymer-Surfactant-Chromophore Co-assembly. J Am Chem Soc 2018; 140:10848-10855. [PMID: 30052038 DOI: 10.1021/jacs.8b05821] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Exploration of triplet-triplet annihilation based photon upconversion (TTA-UC) in aqueous environments faces difficulty such as chromophores insolubility and deactivation of excited triplets by dissolved oxygen molecules. We propose a new strategy of biopolymer-surfactant-chromophore coassembly to overcome these issues. Air-stable TTA-UC with a high upconversion efficiency of 13.5% was achieved in hydrogel coassembled from gelatin, Triton X-100 and upconverting chromophores (triplet sensitizer and emitter). This is comparable to the highest UC efficiency observed to date for air-saturated aqueous UC systems. Moreover, this is the first example of air-stable TTA-UC in the form of hydrogels, widening the applicability of TTA-UC in biological applications. The keys are two-fold. First, gelatin and the surfactant self-assemble in water to give a developed hierarchical structure with hydrophobic domains which accommodate chromophores up to high concentrations. Second, thick hydrogen-bonding networks of gelatin backbone prevent O2 inflow to the hydrophobic interior, as evidenced by long acceptor triplet lifetime of 4.9 ms. Air-stable TTA-UC was also achieved for gelatin with other nonionic surfactants (Tween 80 and Pluronic f127) and Triton X-100 with other gelling biopolymers (sodium alginate and agarose), demonstrating the versatility of current strategy.
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Affiliation(s)
- Pankaj Bharmoria
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS) , Kyushu University , 744 Moto-oka , Nishi-ku , Fukuoka 819-0395 , Japan
| | - Shota Hisamitsu
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS) , Kyushu University , 744 Moto-oka , Nishi-ku , Fukuoka 819-0395 , Japan
| | - Hisanori Nagatomi
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS) , Kyushu University , 744 Moto-oka , Nishi-ku , Fukuoka 819-0395 , Japan
| | - Taku Ogawa
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS) , Kyushu University , 744 Moto-oka , Nishi-ku , Fukuoka 819-0395 , Japan
| | - Masa-Aki Morikawa
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS) , Kyushu University , 744 Moto-oka , Nishi-ku , Fukuoka 819-0395 , Japan
| | - Nobuhiro Yanai
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS) , Kyushu University , 744 Moto-oka , Nishi-ku , Fukuoka 819-0395 , Japan
| | - Nobuo Kimizuka
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS) , Kyushu University , 744 Moto-oka , Nishi-ku , Fukuoka 819-0395 , Japan
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43
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Claereboudt EJS, Eeckhaut I, Lins L, Deleu M. How different sterols contribute to saponin tolerant plasma membranes in sea cucumbers. Sci Rep 2018; 8:10845. [PMID: 30022094 PMCID: PMC6052070 DOI: 10.1038/s41598-018-29223-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 05/25/2018] [Indexed: 12/22/2022] Open
Abstract
Sea cucumbers produce saponins as a chemical defense mechanism, however their cells can tolerate the cytotoxic nature of these chemicals. To elucidate the molecular mechanisms behind this tolerance a suite of complementary biophysical tools was used, firstly using liposomes for in vitro techniques then using in silico approaches for a molecular-level insight. The holothuroid saponin Frondoside A, caused significantly less permeabilization in liposomes containing a Δ7 holothuroid sterol than those containing cholesterol and resulted in endothermic interactions versus exothermic interactions with cholesterol containing liposomes. Lipid phases simulations revealed that Frondoside A has an agglomerating effect on cholesterol domains, however, induced small irregular Δ7 sterol clusters. Our results suggest that the structural peculiarities of holothuroid sterols provide sea cucumbers with a mechanism to mitigate the sterol-agglomerating effect of saponins, and therefore to protect their cells from the cytotoxicity of the saponins they produce.
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Affiliation(s)
- Emily J S Claereboudt
- Biology of marine organisms and biomimetics, Research Institute for Biosciences, University of Mons, B-7000, Mons, Belgium
- Laboratory of molecular biophysics of interfaces, Gembloux Agro-Bio Tech, University of Liege, B-5030, Gembloux, Belgium
| | - Igor Eeckhaut
- Biology of marine organisms and biomimetics, Research Institute for Biosciences, University of Mons, B-7000, Mons, Belgium
| | - Laurence Lins
- Laboratory of molecular biophysics of interfaces, Gembloux Agro-Bio Tech, University of Liege, B-5030, Gembloux, Belgium
| | - Magali Deleu
- Laboratory of molecular biophysics of interfaces, Gembloux Agro-Bio Tech, University of Liege, B-5030, Gembloux, Belgium.
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44
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Ochnio ME, Martínez JH, Allievi MC, Palavecino M, Martínez KD, Pérez OE. Proteins as Nano-Carriers for Bioactive Compounds. The Case of 7S and 11S Soy Globulins and Folic Acid Complexation. Polymers (Basel) 2018; 10:polym10020149. [PMID: 30966185 PMCID: PMC6415263 DOI: 10.3390/polym10020149] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/29/2018] [Accepted: 02/01/2018] [Indexed: 12/29/2022] Open
Abstract
Isolated 7S and 11S globulins obtained from defeated soy flour were complexated with folic acid (FA) in order to generate nano-carriers for this important vitamin in human nutrition. Fluorescence spectroscopy and dynamic light scattering were applied to follow the nano-complexes formation and for their characterization. Fluorescence experimental data were modeled by the Stern-Volmer and a modified double logarithm approach. The results obtained confirmed static quenching. The number of binding sites on the protein molecule was ~1. The values obtained for the binding constants suggest a high affinity between proteins and FA. Particle size distribution allowed to study the protein aggregation phenomenon induced by FA bound to the native proteins. Z-average manifested a clear trend to protein aggregation. 11S-FA nano-complexes resulted in more polydispersity. ζ-potential of FA nano-complexes did not show a remarkable change after FA complexation. The biological activity of nano-complexes loaded with FA was explored in terms of their capacity to enhance the biomass formation of Lactobacillus casei BL23. The results concerning to nano-complexes inclusion in culture media showed higher bacterial growth. Such a result was attributed to the entry of the acid by the specific receptors concomitantly by the peptide receptors. These findings have technological impact for the use of globulins-FA based nano-complexes in nutraceutical, pharmaceutical and food industries.
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Affiliation(s)
- María Emilia Ochnio
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Intendente Güiraldes, s/n, Ciudad Universitaria, Buenos Aires CP 1428, Argentina.
| | - Jimena H Martínez
- Consejo Nacional de Investigación Científica y Técnicas de la República Argentina IQUIBICEN-CONICET, Universidad de Buenos Aires, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Intendente Güiraldes, s/n, Ciudad Universitaria, Buenos Aires CP 1428, Argentina.
| | - Mariana C Allievi
- Consejo Nacional de Investigación Científica y Técnicas de la República Argentina IQUIBICEN-CONICET, Universidad de Buenos Aires, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Intendente Güiraldes, s/n, Ciudad Universitaria, Buenos Aires CP 1428, Argentina.
| | - Marcos Palavecino
- Consejo Nacional de Investigación Científica y Técnicas de la República Argentina IQUIBICEN-CONICET, Universidad de Buenos Aires, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Intendente Güiraldes, s/n, Ciudad Universitaria, Buenos Aires CP 1428, Argentina.
| | - Karina D Martínez
- Consejo Nacional de Investigación Científica y Técnicas de la República Argentina, CONICET, Universidad de Buenos Aires, Departamento de Industrias, Facultad de Ciencias Exactas y Naturales, Intendente Güiraldes, s/n, Ciudad Universitaria, Buenos Aires CP 1428, Argentina.
| | - Oscar E Pérez
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Intendente Güiraldes, s/n, Ciudad Universitaria, Buenos Aires CP 1428, Argentina.
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45
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Chen F, Liu H, Sun H, Pan P, Li Y, Li D, Hou T. Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein-protein binding free energies and re-rank binding poses generated by protein-protein docking. Phys Chem Chem Phys 2018; 18:22129-39. [PMID: 27444142 DOI: 10.1039/c6cp03670h] [Citation(s) in RCA: 309] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Understanding protein-protein interactions (PPIs) is quite important to elucidate crucial biological processes and even design compounds that interfere with PPIs with pharmaceutical significance. Protein-protein docking can afford the atomic structural details of protein-protein complexes, but the accurate prediction of the three-dimensional structures for protein-protein systems is still notoriously difficult due in part to the lack of an ideal scoring function for protein-protein docking. Compared with most scoring functions used in protein-protein docking, the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) methodologies are more theoretically rigorous, but their overall performance for the predictions of binding affinities and binding poses for protein-protein systems has not been systematically evaluated. In this study, we first evaluated the performance of MM/PBSA and MM/GBSA to predict the binding affinities for 46 protein-protein complexes. On the whole, different force fields, solvation models, and interior dielectric constants have obvious impacts on the prediction accuracy of MM/GBSA and MM/PBSA. The MM/GBSA calculations based on the ff02 force field, the GB model developed by Onufriev et al. and a low interior dielectric constant (εin = 1) yield the best correlation between the predicted binding affinities and the experimental data (rp = -0.647), which is better than MM/PBSA (rp = -0.523) and a number of empirical scoring functions used in protein-protein docking (rp = -0.141 to -0.529). Then, we examined the capability of MM/GBSA to identify the possible near-native binding structures from the decoys generated by ZDOCK for 43 protein-protein systems. The results illustrate that the MM/GBSA rescoring has better capability to distinguish the correct binding structures from the decoys than the ZDOCK scoring. Besides, the optimal interior dielectric constant of MM/GBSA for re-ranking docking poses may be determined by analyzing the characteristics of protein-protein binding interfaces. Considering the relatively high prediction accuracy and low computational cost, MM/GBSA may be a good choice for predicting the binding affinities and identifying correct binding structures for protein-protein systems.
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Affiliation(s)
- Fu Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Hui Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Huiyong Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Peichen Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China. and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
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46
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Chakraborty G, Ray AK, Singh PK, Pal H. A highly fluorescent turn-on probe in the near-infrared region for albumin quantification in serum matrix. Chem Commun (Camb) 2018; 54:8383-8386. [DOI: 10.1039/c8cc05058a] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A commercially available styryl based fluorophore in the near-IR region shows exceptional turn-on emission for serum albumins.
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Affiliation(s)
- Goutam Chakraborty
- Laser & Plasma Technology Division
- Bhabha Atomic Research Centre
- Mumbai 400085
- India
- Homi Bhabha National Institute
| | - Alok K. Ray
- Laser & Plasma Technology Division
- Bhabha Atomic Research Centre
- Mumbai 400085
- India
- Homi Bhabha National Institute
| | - Prabhat K. Singh
- Homi Bhabha National Institute
- Training School Complex
- Anushaktinagar
- Mumbai 400094
- India
| | - Haridas Pal
- Homi Bhabha National Institute
- Training School Complex
- Anushaktinagar
- Mumbai 400094
- India
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47
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Huang Y, Zhao L, Keller AA. Interactions, Transformations, and Bioavailability of Nano-Copper Exposed to Root Exudates. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:9774-9783. [PMID: 28771344 DOI: 10.1021/acs.est.7b02523] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Due to the potential for interactions between crop plants and engineered nanomaterials (ENMs), there is increasing interest in understanding the bioavailability and effects of ENMs released into soil systems. Here, we investigate the influence of root exudates on the fate of ENMs from a thermodynamic perspective. Nano isothermal titration calorimetry was applied to determine thermodynamic parameters for the interaction between nanocopper (nCu) and synthetic root exudate (SRE) and its components (including sugars, organic acids, amino acids, and phenolic acids), as well as Cu2+ and SRE. The measured binding constant (Kd = 5.645 × 103 M-1) indicated strong interactions between nCu particles and SRE, as well as with individual organic acids. The interaction between Cu2+ and SRE was stronger (Kd = 7.181 × 104 M-1) but varies for the individual SRE components. nCu dissolution in the presence of SRE was the predominant interaction. In addition, SRE resulted in a complex transformation of nCu, where Cu2+, Cu+, and Cu0 were formed via oxidation and reduction. Plant-nCu exposure experiments indicate that the binding of SRE with nCu and dissolved Cu ions can significantly decrease Cu uptake and bioaccumulation in plants. nITC provides a fundamental thermodynamic understanding of interactions between nCu and plant root exudates, providing an important tool for understanding plant NP-interactions.
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Affiliation(s)
- Yuxiong Huang
- Bren School of Environmental Science and Management, University of California at Santa Barbara , Santa Barbara, California 93106, United States
- Center for Environmental Implications of Nanotechnology, University of California , Santa Barbara, California 93106, United States
| | - Lijuan Zhao
- Bren School of Environmental Science and Management, University of California at Santa Barbara , Santa Barbara, California 93106, United States
- Center for Environmental Implications of Nanotechnology, University of California , Santa Barbara, California 93106, United States
| | - Arturo A Keller
- Bren School of Environmental Science and Management, University of California at Santa Barbara , Santa Barbara, California 93106, United States
- Center for Environmental Implications of Nanotechnology, University of California , Santa Barbara, California 93106, United States
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48
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Li D, Chen L, Wang R, Liu R, Ge G. Synergetic Determination of Thermodynamic and Kinetic Signatures Using Isothermal Titration Calorimetry: A Full-Curve-Fitting Approach. Anal Chem 2017; 89:7130-7138. [DOI: 10.1021/acs.analchem.7b01091] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Dexing Li
- CAS Key Laboratory
of Standardization
and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Lan Chen
- CAS Key Laboratory
of Standardization
and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Ruimin Wang
- CAS Key Laboratory
of Standardization
and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Renxiao Liu
- CAS Key Laboratory
of Standardization
and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Guanglu Ge
- CAS Key Laboratory
of Standardization
and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
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49
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Niroomand H, Mukherjee D, Khomami B. Tuning the photoexcitation response of cyanobacterial Photosystem I via reconstitution into Proteoliposomes. Sci Rep 2017; 7:2492. [PMID: 28559589 PMCID: PMC5449388 DOI: 10.1038/s41598-017-02746-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/19/2017] [Indexed: 12/25/2022] Open
Abstract
The role of natural thylakoid membrane housing of Photosystem I (PSI), the transmembrane photosynthetic protein, in its robust photoactivated charge separation with near unity quantum efficiency is not fundamentally understood. To this end, incorporation of suitable protein scaffolds for PSI incorporation is of great scientific and device manufacturing interest. Areas of interest include solid state bioelectronics, and photoelectrochemical devices that require bio-abio interfaces that do not compromise the photoactivity and photostability of PSI. Therefore, the surfactant-induced membrane solubilization of a negatively charged phospholipid (DPhPG) with the motivation of creating biomimetic reconstructs of PSI reconstitution in DPhPG liposomes is studied. Specifically, a simple yet elegant method for incorporation of PSI trimeric complexes into DPhPG bilayer membranes that mimic the natural thylakoid membrane housing of PSI is introduced. The efficacy of this method is demonstrated via absorption and fluorescence spectroscopy measurements as well as direct visualization using atomic force microscopy. This study provides direct evidence that PSI confinements in synthetic lipid scaffolds can be used for tuning the photoexcitation characteristics of PSI. Hence, it paves the way for development of fundamental understanding of microenvironment alterations on photochemical response of light activated membrane proteins.
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Affiliation(s)
- Hanieh Niroomand
- Sustainable Energy Education and Research Center (SEERC), Knoxville, USA.,Department of Chemical and Biomolecular Engineering, Knoxville, USA
| | - Dibyendu Mukherjee
- Sustainable Energy Education and Research Center (SEERC), Knoxville, USA. .,Department of Chemical and Biomolecular Engineering, Knoxville, USA. .,Department of Mechanical, Aerospace and Biomedical Engineering, University of Tennessee, Knoxville, USA.
| | - Bamin Khomami
- Sustainable Energy Education and Research Center (SEERC), Knoxville, USA. .,Department of Chemical and Biomolecular Engineering, Knoxville, USA. .,Department of Mechanical, Aerospace and Biomedical Engineering, University of Tennessee, Knoxville, USA.
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50
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Spyrakis F, Ahmed MH, Bayden AS, Cozzini P, Mozzarelli A, Kellogg GE. The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery. J Med Chem 2017; 60:6781-6827. [PMID: 28475332 DOI: 10.1021/acs.jmedchem.7b00057] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The value of thoroughly understanding the thermodynamics specific to a drug discovery/design study is well known. Over the past decade, the crucial roles of water molecules in protein structure, function, and dynamics have also become increasingly appreciated. This Perspective explores water in the biological environment by adopting its point of view in such phenomena. The prevailing thermodynamic models of the past, where water was seen largely in terms of an entropic gain after its displacement by a ligand, are now known to be much too simplistic. We adopt a set of terminology that describes water molecules as being "hot" and "cold", which we have defined as being easy and difficult to displace, respectively. The basis of these designations, which involve both enthalpic and entropic water contributions, are explored in several classes of biomolecules and structural motifs. The hallmarks for characterizing water molecules are examined, and computational tools for evaluating water-centric thermodynamics are reviewed. This Perspective's summary features guidelines for exploiting water molecules in drug discovery.
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Affiliation(s)
- Francesca Spyrakis
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino , Via Pietro Giuria 9, 10125 Torino, Italy
| | - Mostafa H Ahmed
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University , Richmond, Virginia 23298-0540, United States
| | - Alexander S Bayden
- CMD Bioscience , 5 Science Park, New Haven, Connecticut 06511, United States
| | - Pietro Cozzini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Laboratorio di Modellistica Molecolare, Università degli Studi di Parma , Parco Area delle Scienze 59/A, 43121 Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Scienze degli Alimenti e del Farmaco, Laboratorio di Biochimica, Università degli Studi di Parma , Parco Area delle Scienze 23/A, 43121 Parma, Italy.,Istituto di Biofisica, Consiglio Nazionale delle Ricerche , Via Moruzzi 1, 56124 Pisa, Italy
| | - Glen E Kellogg
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University , Richmond, Virginia 23298-0540, United States
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